Re: [Open Babel] Translation of crystallographic coordinates into Cartesian

[Vincent Favre-N. <vi...@us...>]

Le 06/04/2011 17:16, Geoffrey Hutchison a écrit :
>> translate coordinates, according to the formula introduced in the
>> International Tables for Crystallography (2006, Vol. B, chapter 3.3), the
>> results are different from those that your program gives.
> 
> Throughout the development of Open Babel, this is one area that has always made me a little afraid. It always seemed a little arbitrary how you pick the rotation matrix for fractional to Cartesian. I had even asked a few crystallographers in the various academic departments and no one could point me to a standard conversion.
> 
> So if you'd like to suggest a different formula, we'd be happy to use it. I suspect the difference is simply a difference in orientation.

  Yes, there is an arbitrary decision when at least one angle is not
equal to 90° - the convention used in OB is an x axis parallel to a, y
axis in the (a,b) plane (not necessarily along b if gamma is not 90°),
and z parallel to c* to finish the orthonormal reference frame. The OB
matrix is :
http://vincefn.net/ObjCryst/form_37.png

  In the IT tables volume B §3.3 there are 3 'usual' conventions listed
(the 3rd only for rhomboedral cells) - the one used in OB is the 2nd one
listed.

  Which one did you use ? Could you give us a CIF file, the matrix that
you used and the pdb file you generated ?

	Vincent